Experiment set4IT024 for Pantoea sp. MT58
nitrogen source Sodium nitrate 5mM
Group: nitrogen sourceMedia: RCH2_defined_Glucose_noNitrogen + Sodium nitrate (5 mM), pH=7
Culturing: MT058_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 30-Jul-20
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Specific Phenotypes
For 12 genes in this experiment
For nitrogen source Sodium nitrate in Pantoea sp. MT58
For nitrogen source Sodium nitrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Nitrate and nitrite ammonification | 7 |
| Coenzyme B12 biosynthesis | 1 |
| Cyanate hydrolysis | 1 |
| Dissimilatory nitrite reductase | 1 |
| Experimental tye | 1 |
| Heme and Siroheme Biosynthesis | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Porphyrin and chlorophyll metabolism
- Nitrogen metabolism
- Phenylalanine, tyrosine and tryptophan biosynthesis
- Biosynthesis of phenylpropanoids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| siroheme biosynthesis | 4 | 4 | 4 |
| alkylnitronates degradation | 2 | 1 | 1 |
| β-alanine degradation III | 2 | 1 | 1 |
| nitrate reduction V (assimilatory) | 2 | 1 | 1 |
| factor 430 biosynthesis | 7 | 3 | 3 |
| uracil degradation III | 5 | 5 | 1 |
| cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion) | 15 | 3 | 3 |
| L-tryptophan biosynthesis | 6 | 6 | 1 |
| cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation) | 13 | 2 | 2 |
| adenosylcobalamin biosynthesis I (anaerobic) | 36 | 12 | 3 |
| superpathway of L-tryptophan biosynthesis | 13 | 13 | 1 |
| 3-hydroxypropanoate cycle | 13 | 6 | 1 |
| glyoxylate assimilation | 13 | 5 | 1 |
| adenosylcobalamin biosynthesis II (aerobic) | 33 | 13 | 2 |
| superpathway of aromatic amino acid biosynthesis | 18 | 18 | 1 |
| 3-hydroxypropanoate/4-hydroxybutanate cycle | 18 | 9 | 1 |
| superpathway of the 3-hydroxypropanoate cycle | 18 | 6 | 1 |
| superpathway of chorismate metabolism | 59 | 44 | 1 |